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Errors in both registration and segmentation #42

@FS-1983

Description

@FS-1983

After fixing the eroor message as posted in my other issue from today, I tried to use the tool again. I'm on Win10 using slicer 5.0.3.
After running, there is now a cropped copy of the fixed volume. From processing, this is the parse:

Processing started
CASE_1_MRI_ISO
CASE1_1_CT_ISO
 Defaults paths: 
      VisSimTools folder: C:\Users\Flori\VisSimTools
      Output folder     : C:\Users\Flori\VisSimTools\outputs
      elastix binaries are found in C:\ProgramData\NA-MIC\Slicer 5.0.3\NA-MIC\Extensions-30893\SlicerElastix\lib\Slicer-5.0/elastix.exe
      Cochlea Extension is selected
      sha256computedCheckSum: d9db4206e2b0abdbf9a160cecde47eedc9da2cc593ce8601900d47c4c05de422
      Models or contents are wrong, trying to download ...
      Downloading VisSim Tools  ... 
      Downloading VisSimTools others ...
     Extracting to user home 
      Error: can not download and extract VisSimTools ...
Destination path 'C:\Users\Flori/VisSimTools\VisSimToolsCochlea' already exists
0
<class 'vtkSlicerMarkupsModuleMRML.vtkMRMLMarkupsFiducialNode'>
run fixed point: ============================
CASE_1_MRI_ISO
[483 357  65]
0
<class 'vtkSlicerMarkupsModuleMRML.vtkMRMLMarkupsFiducialNode'>
run moving point: ============================
CASE1_1_CT_ISO
[718 617 122]
=================== Cropping =====================
================= Begin cropping  ... =====================
 location: [483,357,65]   cropping length: [ 10 , 10 , 10 ]
[ 10 , 10 , 10 ]
[ 0.125, 0.125 , 0.125 ]
[483,357,65]
location: [483.0, 357.0, 65.0]   cropping length: [10.0, 10.0, 10.0]
Cropping with [459, 333, 41] and [143, 269, 61].
cropped:     C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd
iso cropped: C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_CropIso.nrrd
C:\ProgramData\NA-MIC\Slicer 5.0.3\Slicer --launch C:\ProgramData\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\cli-modules\ResampleScalarVolume
10752
Executing ... C:\ProgramData\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\cli-modules\ResampleScalarVolume.exe -i linear -s  [0.125,0.125,0.125] C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_CropIso.nrrd
 Cropping and resampling are done !!! 
 Cropped image is saved in : [C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd]
 Cropping is done !!! 
Traceback (most recent call last):
  File "C:/ProgramData/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/SlicerCochlea/lib/Slicer-5.0/qt-scripted-modules/CochleaReg.py", line 219, in onApplyBtnClick
    registeredMovingVolumeNode =self.logic.run( self.fixedSelectorCoBx.currentNode(),self.fixedFiducialNode, self.movingSelectorCoBx.currentNode(),self.movingFiducialNode )
  File "C:/ProgramData/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/SlicerCochlea/lib/Slicer-5.0/qt-scripted-modules/CochleaReg.py", line 310, in run
    [success, croppedFixedNode] = slicer.util.loadVolume(self.vsc.vtVars['fixedCropPath'])
TypeError: cannot unpack non-iterable MRMLCore.vtkMRMLScalarVolumeNode object

Now, when I try to use the segment, I get a different error message:

Processing started
 Defaults paths: 
      VisSimTools folder: C:\Users\Flori\VisSimTools
      Output folder     : C:\Users\Flori\VisSimTools\outputs
      elastix binaries are found in C:\ProgramData\NA-MIC\Slicer 5.0.3\NA-MIC\Extensions-30893\SlicerElastix\lib\Slicer-5.0/elastix.exe
      Cochlea Extension is selected
      sha256computedCheckSum: d9db4206e2b0abdbf9a160cecde47eedc9da2cc593ce8601900d47c4c05de422
      Models or contents are wrong, trying to download ...
      Downloading VisSim Tools  ... 
      Downloading VisSimTools others ...
     Extracting to user home 
      Error: can not download and extract VisSimTools ...
Destination path 'C:\Users\Flori/VisSimTools\VisSimToolsCochlea' already exists
inputVolumeNode       =  CASE_1_MRI_ISO
inputFiducialNode     =  CASE_1_MRI_ISO_CochleaLocation
outputPath            =  C:\Users\Flori\VisSimTools\outputs
parsPath              =  C:\Users\Flori\VisSimTools\pars\parCochSeg.txt
0
<class 'vtkSlicerMarkupsModuleMRML.vtkMRMLMarkupsFiducialNode'>
=================== Cropping =====================
================= Begin cropping  ... =====================
 location: [483,352,71]   cropping length: [ 10 , 10 , 10 ]
[ 10 , 10 , 10 ]
[ 0.125, 0.125 , 0.125 ]
[483,352,71]
location: [483.0, 352.0, 71.0]   cropping length: [10.0, 10.0, 10.0]
Cropping with [459, 328, 47] and [143, 274, 55].
cropped:     C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd
iso cropped: C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_CropIso.nrrd
C:\ProgramData\NA-MIC\Slicer 5.0.3\Slicer --launch C:\ProgramData\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\cli-modules\ResampleScalarVolume
10752
Executing ... C:\ProgramData\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\cli-modules\ResampleScalarVolume.exe -i linear -s  [0.125,0.125,0.125] C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_CropIso.nrrd
 Cropping and resampling are done !!! 
 Cropped image is saved in : [C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd]
 Cropping is done !!! 
=================== Registration =====================
************  Rigid Registeration: model to cropped input image **********************
************  Compute the Transform **********************
win32
 elastix is running in Windows :( !!!
C:\ProgramData\NA-MIC\Slicer 5.0.3\NA-MIC\Extensions-30893\SlicerElastix\lib\Slicer-5.0/elastix.exe -f C:\Users\Flori\VisSimTools\CASE_1_MRI_ISO_Crop.nrrd -m C:\Users\Flori\VisSimTools\models\modelCochlea\MdlDvLc.nrrd -out C:\Users\Flori\VisSimTools\outputs -p C:\Users\Flori\VisSimTools\pars\parCochSeg.txt
1
No error!
Traceback (most recent call last):
  File "C:/ProgramData/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/SlicerCochlea/lib/Slicer-5.0/qt-scripted-modules/CochleaSeg.py", line 244, in onApplyBtnClick
    self.logic.run( self.inputSelectorCoBx.currentNode(),self.logic.inputFiducialNode, self.vsc.vtVars['cochleaSide'] )
  File "C:/ProgramData/NA-MIC/Slicer 5.0.3/NA-MIC/Extensions-30893/SlicerCochlea/lib/Slicer-5.0/qt-scripted-modules/CochleaSeg.py", line 365, in run
    os.rename(resImgPathOld,resImgRgPath)
FileNotFoundError: [WinError 2] Het systeem kan het opgegeven bestand niet vinden: 'C:\\Users\\Flori\\VisSimTools\\outputs\\result.0.nrrd' -> 'C:\\Users\\Flori\\VisSimTools\\outputs\\result.Rg.nrrd' 

Again, thanks for any help!

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